As a new president, he dismissed the idea of American exceptionalism, noting that Greeks think their country is special, too. He labeled the Bush-era interrogation practices, euphemistically called “harsh” for years, as torture. America, he has suggested, has much to answer given its history in Latin America and the Middle East.

His latest challenge came Thursday at the National Prayer Breakfast. At a time of global anxiety over Islamist terrorism, Obama noted pointedly that his fellow Christians, who make up a vast majority of Americans, should perhaps not be the ones who cast the first stone.

“Humanity has been grappling with these questions throughout human history,” he told the group, speaking of the tension between the compassionate and murderous acts religion can inspire. “And lest we get on our high horse and think this is unique to some other place, remember that during the Crusades and the Inquisition, people committed terrible deeds in the name of Christ. In our home country, slavery and Jim Crow all too often was justified in the name of Christ.”

Some Republicans were outraged. “The president’s comments this morning at the prayer breakfast are the most offensive I’ve ever heard a president make in my lifetime,” said former Virginia governor Jim Gilmore (R). “He has offended every believing Christian in the United States. This goes further to the point that Mr. Obama does not believe in America or the values we all share.”

Obama’s remarks spoke to his unsparing, sometimes controversial, view of the United States — where triumphalism is often overshadowed by a harsh assessment of where Americans must try harder to live up to their own self-image. Only by admitting these shortcomings, he has argued, can we fix problems and move beyond them.

“There is a tendency in us, a sinful tendency, that can pervert and distort our faith,” he said at the breakfast.

But many critics believe that the president needs to focus more on enemies of the United States.

Russell Moore, president of the Southern Baptist Ethics and Religious Liberty Commission, called Obama’s comments about Christianity “an unfortunate attempt at a wrongheaded moral comparison.”

What we need more is a “moral framework from the administration and a clear strategy for defeating ISIS,” he said, using an acronym for the Islamic State.

Farhana Khera, executive director of the civil rights group Muslim Advocates, one of 13 participants, said the session gave Obama a chance to focus on Muslim Americans the way he has done with other constituencies, such as African American and Jewish groups.

“I started off by saying the biggest concern I hear from Muslim parents is their fear that their children will be ashamed to be Muslim” because of discrimination, Khera said. “We are asking him to use his bully pulpit to have a White House summit on hate crimes against religious minorities, much like the summit on bullying reset the conversation around LGBT youth.”

Obama emphasized the need to respect minorities in his speech Thursday, saying it was part of the obligation Americans face as members of a diverse and open society, “And if, in fact, we defend the legal right of a person to insult another’s religion, we’re equally obligated to use our free speech to condemn such insults — and stand shoulder to shoulder with religious communities, particularly religious minorities who are the targets of such attacks.”